groupICA.cifti | R Documentation |
Perform group ICA based on CIFTI data
groupICA.cifti( cifti_fnames, subjects = NULL, brainstructures = c("left", "right"), num_PCs = 100, num_ICs, max_rows_GPCA = 10000, center_Bcols = FALSE, scale = c("global", "local", "none"), scale_sm_FWHM = 2, detrend_DCT = 0, verbose = TRUE, out_fname = NULL, surfL = NULL, surfR = NULL, smooth = TRUE, smooth_surf_FWHM = 5, smooth_vol_FWHM = 5, smooth_zeroes_as_NA = FALSE, smooth_subcortical_merged = FALSE )
cifti_fnames |
Vector of file paths of CIFTI-format fMRI timeseries (*.dtseries.nii) for which to calculate group ICA |
subjects |
Use this argument if some subjects have more than one scan.
This is a numeric or factor vector the same length as |
brainstructures |
Character vector indicating which brain structure(s)
to obtain: |
num_PCs |
Maximum number of PCs to retain in initial subject-level PCA |
num_ICs |
Number of independent components to identify. |
max_rows_GPCA |
The maximum number of rows for the matrix on which group
level PCA will be performed. This matrix is the result of temporal concatenation
and contains |
center_Bcols, scale, scale_sm_FWHM, detrend_DCT |
Center BOLD columns, scale by the
standard deviation, and detrend voxel timecourses? See
|
verbose |
If |
out_fname |
(Optional) If not specified, a xifti object will be returned but the GICA maps will not be written to a CIFTI file. |
surfL |
(Optional) File path to a surface GIFTI for the left cortex. If provided, will be part of xifti result object for visualization in R. Will also be used to perform any smoothing. |
surfR |
(Optional) File path to a surface GIFTI for the right cortex. If provided, will be part of xifti result object for visualization in R. Will also be used to perform any smoothing. |
smooth |
Smooth the CIFTI data prior to reading in each file? Default:
|
smooth_surf_FWHM, smooth_vol_FWHM, smooth_zeroes_as_NA, smooth_subcortical_merged |
See |
out_fname
if a file was written, or the GICA as a "xifti"
object
if not.
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